Visualize all samples and parameters as well as ancestry in a single pane during your analysis.
While analyzing your samples, you may find yourself asking questions like: Do I need to adjust my upstream gates? How does this gate placement look on the rest of my samples? Is this marker co-expressed with anything else? To answer these, it may be helpful to briefly see your data summarized or plotted in different ways. Rather than change the data displayed in your Primary Plot, utilize the various shortcut visualizations in the Graph Gallery (Figure 1).
Figure 1. Graph gallery
Display data
Select Graphs in the Context navigation bar to launch plots in the Discovery panel (Figure 2.1). Next, click the group of samples in the Groups panel that you want to see in the Primary plot and Graph gallery (Figure 2.2). Use the dropdown menu in the Graph gallery to change the display to View by Sample, Parameter, or Ancestry (details in sections below) (Figure 2.3). Adjust the height of the gallery by dragging the gallery’s top border or enter a full screen view by clicking the icon on the top right of the Graph gallery. The Graph properties panel contains controls for customizing graph types and color palettes for both the Primary plot and Graph gallery.
Graphs in the gallery are interactive! Click any graph to quickly display it in the Primary plot above the gallery (Figure 2.4).
Figure 2. Display data in the Graph gallery
View by Sample
This is the default view in the Graph gallery, whereby the graph seen in the Primary plot is shown for every sample in the selected group (Figure 3). In other words, each graph represents a different sample. Use this view to guide gate placement, navigate between samples for quick gate adjustments, or preview marker expression patterns across experimental conditions in your experiment.
In the example below, you can easily see that samples stimulated with PI have downregulated CD3 and CD4, so a gate adjustment on those plots will be needed.
Figure 3. View by Sample
View by Parameter
This view will plot a single parameter against all other parameters in the experiment (Figure 4). Here, all data in the Graph gallery are from a single sample and population (both can be changed by making selections in the Samples pane and Populations pane). The single parameter kept constant across the gallery graphs can be one of two parameters currently shown on the axes of the Primary Plot (Figure 4.1). In the Primary plot below, p-ERK is shown on the x-axis and IFN-g on the y-axis. In the Graph gallery, selecting View By Parameter (Figure 4.2) and Batch X allows the x-axis to iterate across parameters while locking IFN-g on the y-axis. Conversely, selecting Batch Y, iterates the y-axis across parameters while locking p-ERK on the x-axis (Figure 4.3).
Use this view to preview combinatorial phenotypes. In the example below, I can see that CD4 T cells that are IFNg+ are largely negative for other surface activation markers in my panel, like CD38 and HLA-DR. This view can also be helpful for inspecting residual spillover after compensation in full-stain samples or single-stained controls.
Figure 4. View by Parameter
View by Ancestry
This view will show all gated plots upstream of a selected population in a single sample (Figure 5). The depth of the ancestry shown is dictated by the population selected in the Populations pane. In other words, selecting the final population node in your ancestry will reveal the entire upstream gating hierarchy while selecting the top population node will reveal no ancestry because there’s nothing upstream of it.
Use this to review gate placement in your hierarchy across samples or to quickly capture and share your gating strategy with collaborators.
Figure 5. View by Ancestry